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ReleaseTheKraken

Nextflow workflow for taxonomic classification of shotgun metagenomic data with Kraken 2.

Rationale

This workflow performs taxonomic profiling through lowest common ancestor (LCA) positioning approach using Kraken2. In this approach the pre-aligned sequences are hierarchically classified on a taxonomy tree using a placement algorithm. It requires database for comparison with the appropriate taxonomical information so this workflow comes packaged together with the MiniKraken Database.

Implementation

This workflow is implemented in 3 data processing steps: QC, Taxonomic Profiling and Visualization. For each step the following tools are used:

  • QC: fastp
  • Taxonomic profiling: Kraken 2 with Minikraken_8GB_202003 database
  • Visualization: Krona

Usage:

Release the Kraken workflow expects a single sample file (FASTQ), passed with the --fastq parameter, and generates an HTML Krona plot with the taxonomic information. The Kraken report is stored under results/kraken.

Basic run command example

nextflow main.nf --fastq="test_data/SRR8886136_{1,2}*"